Listen to Lara's voice in "Peaceful Days" and how utterly defeated she sounds. That is a woman who is on the edge of the Despair Event Horizon. It becomes inverted in "Epilogue/Moonlight Parade" when her eyes are full of life and her voice full of happiness thanks to Lucca saving her from her accident.
As in the original game, Robo being nearly scrapped by his brother units. Only this time, it's fully voiced.
"The Singing Mountain" can be quite sad because of just how melancholic it is. It becomes even more so when its tune is reprised during "History, Our Story" after the party defeats Magus only to find out he did not create Lavos, only summoned it, leaving them with no idea how to find and destroy it—as their Despair Event Horizon.
Robo: I've seen life and joy forgotten A world where all hope has failed This monster so foul and rotten What chance have we to prevail? Frog: The Fiendlord now lost to history No clues where he'll make his mark This monster remains a mystery And we remain in the dark. Marle: Can we stop this dark hour? Can we escape our fate? Will we all be devoured? Are we always too late?
And then there's "Schala's Theme", which here is turned into a sweet lullaby she sings to little Janus to try and reassure him that despite his premonition of death, and the knowledge they both have of the Mammon Machine and what its power has done to their mother, there is still hope. A perfect encapsulation of the genuine kindness and goodness she possesses...which only makes her ultimate fate all the more heartbreaking.
The song "Depths of Night" is theDespair Event Horizon of the team: Crono is dead, Lavos took Schala and they have lost everything; no one is trying to lift their spirits up and the melody is heartbreaking. It cuts even deeper when you realize that Frog and even Magus are trying to put on a brave face, while Marle, Lucca, Robo and Ayla are openly expressing their grief.
Try to not cry when Crono begs the team to not give up... and they can't hear him.
Another tear-jerker: last time the team was at the Despair Event Horizon, it was Lucca and Crono who pulled them away from it. This time, Crono is dead, and Lucca is too heartbroken to give another Rousing Speech. There's nothing stopping them from crossing it, this time.
"Magus Reprise" in which Magus all but says outright that his life has been nothing but misery and hatred, and all he wants to do is die. And Frog almost obliges before recalling the words of both Crono and Cyrus and realizes that Magus, while not a good man, is as much a victim in this as any of them.
Blackness surrounds the world we defiled! All 'round, you hear the cries of the child! Broken and tossed away and reviled! Hope can never be reconciled!
The very beginning of "Gaspar" when the old man asks where Crono is. Marle's crying tells him all he needs to know.
Atropos's death in "Prometheus Unbound." The fact that her voice becomes more and more distorted makes it all the more heartbreaking.
While its entry in the Awesome subpage isn't undeserved, the first part of "Ozzie's Fort" can be this too from Magus' Generals' point of view; they sound genuinely hurt over not only Magus betraying them, but the revelation that he never cared about them and only used them for his own goals:
Flea: Just another naughty child That we plucked from the wild And left us all behind. Slash: We believed in you And you played us for fools You will pay, you will suffer and die! (...) Slash: Everything you know We taught you, watched you grow And this is how we are repaid?
There's no singing in the visit to Lucca's past. Just a scientist watching her worst memory play back in front of her eyes, and having a brief flashback to the traumatizing way it turned out last time, as this time, she's able to save her mother...
